Scott Soderling
Neuroscientist-cell biologist, proteomics developer, deep learning collaborator, tackling brain disorders. PI @Duke. Chair of Cell Biology and Biochem. Founder, Triangle Protein Design.
http://soderlinglab.cellbio.duke.edu
- Reposted by Scott SoderlingYou can use the model right now to freely generate families for single sequence inputs (i.e., diversification conditioned by intrinsic representations of evolution), or to engineer proteins based on family promts (diversification by conditioning on particular evoluationary trajectories).
- Reposted by Scott Soderling@rohitsingh8080.bsky.social USHER: Guiding Foundation Model Representations through Distribution Shifts Aditya Pratapa, Purushothama Rao Tata, Rohit Singh bioRxiv 2025.11.20.689462; doi: doi.org/10.1101/2025...
- Reposted by Scott SoderlingThe existence of specialized phosphatases in regulating the AIS was unclear. In this initial report, we show that a PP2A subunit is enriched at the AIS and contributes to its local phosphoregulation. Fun collaboration with Dr. Matthew Rasband's lab, and thanks to all authors for their contribution!
- There is nothing sweeter than the first paper from your former postdoc’s own lab. Huge congratulations to Yudong and his lab! www.nature.com/articles/s41...
- Sounds very exciting
- Congratulations to @swcanner.bsky.social for the successful defense of his thesis, “The Protein Sugar Interactome”! Leveraging deep learning and AI, he created tools and uncovered putative structural interactions underlying intercellular communication. He will receive his diploma in December.
- Reposted by Scott SoderlingThe published version of our study on the early-life transition from isolation USVs to adult-like USVs in juvenile mice is out in Animal Behaviour! authors.elsevier.com/a/1m1YDmjMA4GP bsky.app/profile/kati...
- Another study to share, led by my grad student Nicole Pranic! Before diving in, I'll add that Nicole (who is clever, tenacious, and interested in neural changes that underlie developmental changes in social behaviors) is looking for a post-doc position! Please RT! www.biorxiv.org/content/10.1...
- Deadline for applications- November 1st!
- Duke Cell Biology is hiring in AI/ML! @scottsoderling.bsky.social, @rohitsingh8080.bsky.social, and others are building a very active community around ML for discovery science, and Duke is a great place to be. academicjobsonline.org/ajo/jobs/30509
- Reposted by Scott SoderlingWe are hiring!
- Please repost!!: We are searching for new AI-Bio faculty at Duke to be part of a new Discovery AI center. Looking for faculty who focus on pushing boundaries in ML model development in a highly interactive environment. DEADLINE for applications- Nov 1st!! www.nature.com/naturecareer...
- Please repost!!: We are searching for new AI-Bio faculty at Duke to be part of a new Discovery AI center. Looking for faculty who focus on pushing boundaries in ML model development in a highly interactive environment. DEADLINE for applications- Nov 1st!! www.nature.com/naturecareer...
- Reposted by Scott SoderlingI am thrilled to share our latest story led by the incredibly talented Brooke D’Arcy and Camila Musso. We discover a rich world of local gene expression in radial glia, essential neural and glial precursors, and develop a new method for sub-cellular mRNA manipulation. www.biorxiv.org/content/10.1...
- Cool new work- DynamicsPLM adds prot conformational dynamics to LMs: fuses seq with per-residue structure-token distributions from an ensemble (no averaging) → state-aware embeddings. Gains: +4% HumanPPI, +11% on multi-state proteins. Firing this up in the lab soon! www.biorxiv.org/content/10.1...
- Reposted by Scott SoderlingDuke Cell Biology is hiring in AI/ML! @scottsoderling.bsky.social, @rohitsingh8080.bsky.social, and others are building a very active community around ML for discovery science, and Duke is a great place to be. academicjobsonline.org/ajo/jobs/30509
- Duke is recruiting a tenure-track Assistant Professor in AI/ML for Biology—joint Discovery AI Initiative × Cell Biology Search. Building models for protein design, single-cell/spatial omics, imaging, proteomics, genomics? Apply: academicjobsonline.org/ajo/jobs/30509 #hiring #AIforBio #CompBio
- Reposted by Scott SoderlingBuilding a spine is no joke, but thankfully zebrafish have their own clocks to keep the pace. Excited to share our preprint on the role of biological oscillators in coordinating notochord development! (www.biorxiv.org/content/10.1...) Additional thread below
- Reposted by Scott SoderlingPriyom's preprint is out on biorxiv. See below for a detailed thread. In a nutshell, she has discovered and characterized the oscillator that times notochord and spine segmentation in zebrafish. Turns out that there are uniform Erk oscillations across the entire tissue that act as timekeepers!
- Building a spine is no joke, but thankfully zebrafish have their own clocks to keep the pace. Excited to share our preprint on the role of biological oscillators in coordinating notochord development! (www.biorxiv.org/content/10.1...) Additional thread below
- Reposted by Scott SoderlingDuke researchers have uncovered a promising path to potentially treat a family of rare neurodegenerative disease called neurodegeneration with brain iron accumulation (NBIA). 🔗: mgm.duke.edu/news/fundamental-ce… #AcademicSky #MedSky
- Another milestone for the amazing Munjal lab!
- Reposted by Scott SoderlingThe order is the latest move by the Trump administration to assert control over US science go.nature.com/3H6IxVr
- Reposted by Scott SoderlingSharing our newest study led by the incredibly talented @federicamosti.bsky.social investigating new molecular mechanisms of human brain development. We discover a human-specific enhancer HAR1984 that influences chromatin looping to promote cortical size and folding! www.biorxiv.org/cgi/content/...
- Great work from Huanghe Yang’s lab in Duke Biochemistry.
- New research from Duke could transform how complications related to the placenta during pregnancy are detected and prevented. This discovery may also lead to new insights into cancer, bone healing, and viral infections. 🔗 Read more: medschool.duke.edu/news/protein... #AcademicSky #MedSky
- Congrats James! Loved hearing about this at an earlier CZI meeting!
- ⚡️Thrilled that #VirtualLab is published in @nature.com! www.nature.com/articles/s41... We created a team of AI agents to mirror my Stanford lab 🤖. Led by a PI agent, the AI scientists ran their own group meetings and discovered effective binders to new CoVID variants that we validated.
- I like o3 pro even better.
- o3, an AI model developed by the creators of ChatGPT, has been ranked the best AI tool for answering science questions in multiple fields go.nature.com/4lzaWlC
- Reposted by Scott SoderlingSteve Jobs was a vibe coder, he just prompted Steve Wozniak
- Reposted by Scott SoderlingResearchers are making ever more sophisticated mini organs in the lab — and now they can grow their own blood vessels go.nature.com/4nNF3ri
- Reposted by Scott SoderlingThe new Center of Excellence for Multiscale Immune Systems Modeling (MISM), launching soon by Duke University School of Medicine researchers, will transform how we understand and treat infectious and immune-related diseases. #AcademicSky #MedSky
- Lab backpacking trip recently along the AT in NC. It's so nice to get away from it all, together.
- Reposted by Scott SoderlingIn this essay in Hopkins Magazine, I talk about how NIH budget cuts will delay or stop the translation of basic science to the clinic and impact kids with intellectual disability, autism, and epilepsy. hub.jhu.edu/magazine/202...
- AI research in collaboration with cell biologists is transforming research at Duke. More discoveries coming soon!!
- The AI tool Raygun (named as an homage to “Honey, I Shrunk the Kids”) is just one of several tools that a team led by Duke's Rohit Singh, PhD, has built to help scientists work both faster and smarter. 🔗 Read more: medschool.duke.edu/stories/hone... #DukeB&B #DukeCellBiology #AcademicSky #MedSky
- Reposted by Scott SoderlingThe AI tool Raygun (named as an homage to “Honey, I Shrunk the Kids”) is just one of several tools that a team led by Duke's Rohit Singh, PhD, has built to help scientists work both faster and smarter. 🔗 Read more: medschool.duke.edu/stories/hone... #DukeB&B #DukeCellBiology #AcademicSky #MedSky
- Reposted by Scott SoderlingCongrats to HHMI Freeman Hrabowski Scholars @channyskye.bsky.social , Josefina del Mármol (@delmarmollab.bsky.social), @yvetteefisher.bsky.social and Theanne Griffith (@doctheagrif.bsky.social), named 2025 McKnight Scholars for their demonstrated commitment to neuroscience & mentoring others! 🌟
- Reposted by Scott SoderlingExcited to be joining a fantastic community of neuroscientists!
- Congrats to HHMI Freeman Hrabowski Scholars @channyskye.bsky.social , Josefina del Mármol (@delmarmollab.bsky.social), @yvetteefisher.bsky.social and Theanne Griffith (@doctheagrif.bsky.social), named 2025 McKnight Scholars for their demonstrated commitment to neuroscience & mentoring others! 🌟
- Reposted by Scott SoderlingShuo Han, PhD, a Duke biochemist, is leading research to decode the gut microbiome’s chemical language. Her lab has released a free protocol that helps researchers detect over 800 gut-derived metabolites. 🔗 Read more: www.biochem.duke.edu/news/secret-... #DukeBiochemistry #AcademicSky #MedSky
- Looking forward to reading this.
- With contributions from fantastic colleagues @martinsteinegger.bsky.social , @mikeinouye.bsky.social, @jlistgarten.bsky.social , @ideasbyjin.bsky.social, @michael-heinzinger.bsky.social, and many more, the first CSHL volume on ML for Protein Science and Engineering is out: lnkd.in/dQdgGPpp
- Reposted by Scott SoderlingExcited to share our Science paper on HaloDA1.0-the first genetically encoded far-red dopamine sensor! 🥳It enables powerful multiplex imaging in neurons, brain slices, and live animals.🧠🔬 #GRABsensors #Dopamine www.science.org/doi/10.1126/...
- Reposted by Scott SoderlingAurora alert! It’s possible the aurora boralis may be visible tonight as far south as Alabama. Start looking tonight after dark around 10 pm (I’ve attached both the NOAA and University of Alaska maps, the former is always very conservative with view lines) www.swpc.noaa.gov/communities/...
- Reposted by Scott SoderlingPostdoc opportunity in the heart of Europe! Check out the flyer below. Join our team on an international project with Anthony Holtmaat exploring synaptic plasticity and specificity in cortical and thalamocortical circuits.
- Reposted by Scott SoderlingThe unintended consequence of….. www.nytimes.com/2025/05/30/o...
- Reposted by Scott SoderlingGlad to see our new paper finally out! We show how the GPR158 receptor controls synapse maturation and function by silencing an intrinsic inhibitory mechanism. authors.elsevier.com/a/1l7HS5Sx5g... Work from Ben Verpoort and colleagues, with special thanks to our collaborators.
- 🧠 New in Nature from the fabulous Silver Lab @ Duke: A human-specific enhancer, HARE5, boosts radial glia proliferation, expanding neocortical size and connectivity. Knock-in mice showed enlarged cortices and more neurons. This highlights how regulatory DNA changes shaped human brain evolution.
- Thrilled to share our latest study out in @natureportfolio.nature.com led by the fantastically talented Jing Liu. Our study provides insight into a long standing question in biology: What molecular features make us uniquely human and how do these function? www.nature.com/articles/s41...
- Reposted by Scott Soderling
- Reposted by Scott SoderlingIntroducing KolossuS to address a 50-year old problem: which kinases are active in your pathway of interest? As computational biologists, our work mostly involves post-hoc analysis algorithms. KolossuS is the rare case where a ML model enables entirely new capabilities. 1/
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View full threadReposted by Scott SoderlingThis was a wonderful collab with @scottsoderling.bsky.social , whose lab is situated next to ours. If you want to do cool collaborative work like this, join us! We're building a great ecosystem of AIxBio at Duke.
- Reposted by Scott SoderlingOne of grants frozen at Cornell: $6.7M (4 yrs) to develop heart pumps for babies born w/ heart defects. It took decades of work to get to point of prepping device for in-human clinical trials. No private company could do this. The cruelty of the Trump administration is heartbreaking. So to speak.
- Just snagged some tickets for the upcoming Pearl Jam concert in Raleigh NC. SO EXCITED!
- Over 50 yrs since the discovery of protein kinases, 80% of human kinases still have ≤20 known substrates, and many are “dark.” I'm EXCITED to announce our new work towards solving this- combining (1) deep learning with (2) proximity proteomics in vivo! ➡️ www.biorxiv.org/content/10.1...
- (1) Our deep learning model, KolossuS, leverages large protein language models to learn the “grammar” of kinase–substrate recognition, achieving SOTA accuracy and performance across the mammalian kinomes. It is well-calibrated across kinase families, enabling real-world usage.
- (2) It is insufficient to simply predict kinase specificities in vitro; kinases must also meet their substrates in cellular contexts. We tag endogenous kinases with TurboID in mouse brain, capturing substrates within ~10 nm in living animals.
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View full threadThe BEST part: This would not have been possible without the close (and SO FUN!) collaboration of my lab with @rohitsingh8080.bsky.social and the lab of Masashi Yanagisawa.
- Just had to share a proud dad moment—my son has published his first paper! 🎉 www.cureus.com/articles/354...
- Eye opening. Highly recommend. Research is intentional collateral damage in the service of a larger ideological goal.
- Required Listening www.nytimes.com/2025/04/11/p...
- Reposted by Scott SoderlingPublished an op-ed for @cnn.com: “Nobel laureate: I owe America my success. Today, its scientific future is in danger.” A personal reflection on what’s at stake as science funding gets slashed. I’d be grateful if you could amplify both in and beyond the science world. www.cnn.com/2025/04/09/h...
- Reposted by Scott SoderlingOur work on better ways of aggregating PLM embeddings is now out in Bioinformatics Advances.
- This NIH policy was rescinded on Friday: grants.nih.gov/grants/guide...
- Key points gutted: It is the policy of NIH to: 1. Prohibit political interference or other inappropriate influence in the design, proposal, conduct, review, management, evaluation, communication of, and use of scientific activities and scientific information conducted by covered individuals.
- 3. Require that leadership and management ensure that covered individuals engaged in scientific activities can conduct their work objectively, free from political interference or other inappropriate influence, and free from retaliation.
- Reposted by Scott Soderling[This post could not be retrieved]
- Reposted by Scott SoderlingScience under siege: protecting scientific progress in turbulent times journals.biologists.com/dev/article/...
- Reposted by Scott SoderlingNice News & Views on our recent paper from Tim Saunders. www.nature.com/articles/s41...
- Reposted by Scott SoderlingYes, everything is on fire, but also we did some neat science. Read @schreinerdrew.bsky.social’s excellent breakdown here. tl;dr: we can track learning of birdsong on a syllable-by-syllable basis, and yes, dopamine tracks better-than-recent performance, but it’s more interesting than you’d think!
- Proud to have contributed to @jiaxuanqi.bsky.social's masterpiece out @nature.com! She shows that dopamine transients track the learned quality of song during juvenile learning and that dopamine release is driven not just by VTA firing, but by a local cholinergic mechanism! (1/x)
- Excited to share exciting new work from my former postdoc, Il Hwan Kim. His study reveals that SHANK3, an ASD-risk gene, is expressed in brain endothelial cells and plays a crucial role in maintaining tight junction integrity at the blood-brain barrier. www.nature.com/articles/s41...
- Reposted by Scott SoderlingA nation that turns its back on science risks losing its humanity, today’s funding cuts are tomorrow’s crises.
- Reposted by Scott SoderlingThat’s right. The lessons we learn as scientists — to keep trying things in the face of uncertainty, to be ok with failure and be persistent — are important for us now as we seek to stop this ongoing coup.
- Reposted by Scott Soderling
- Reposted by Scott SoderlingWelcome to the Bluesky account for Stand Up for Science 2025! Keep an eye on this space for updates, event information, and ways to get involved. We can't wait to see everyone #standupforscience2025 on March 7th, both in DC and locations nationwide! #scienceforall #sciencenotsilence
- Reposted by Scott SoderlingOur paper, led by @argo-mkhrji.bsky.social and @woonyunghur.bsky.social, on cortical migration of nuclei in drosophila embryos came out today in @naturephysics.bsky.social. Argo wrote a comprehensive thread below. A great collaboration with Massimo Vergassola and @streichan.bsky.social.
- 1/n Wanted to share this latest piece of work that came online today on how Scale-independent and Topological interactions govern the spindle orientation and in turn the decision to become embryonic/yolk nuclei. Freely available to read here: rdcu.be/ebb0l
- Reposted by Scott SoderlingTwo major life updates: - I'm moving to Senior Applied Research Scientist in Digital Biology at NVIDIA (Jan '25) - I'm starting a new lab at Duke as Visiting Assistant Prof (early '25) Both roles focus on tackling hard problems in biological machine learning through collaborative research. Long 🧵
- Reposted by Scott SoderlingAbMAP, our work on adapting PLMs for antibodies, is now out in @pnas.org A veritable zoo of PLMs now exists, so why should you care? Well, AbMAP reflects an opinionated design philosophy about antibody representation. And based on your needs, it may be a great fit! 1/ www.pnas.org/doi/10.1073/...
- Reposted by Scott SoderlingLikewise, I’m extremely thankful to David Page and @scottsoderling.bsky.social at Duke, who have recognised that biology and information sciences are increasingly intertwined, with software programmable biology becoming a reality through ML informed by passionate and knowledgable (cell) biologists.
- Reposted by Scott SoderlingTruly honored that our work was highlighted as one of many applications where #Alphafold has had an enormous impact
- Yesterday, #DemisHassabis delivered his #Nobel Prize Lecture & referenced a paper on 1st contact between egg and sperm by our @pauligroup.bsky.social, @vdeneke.bsky.social, Andreas Blaha, et al. The study was highlighted as a user case for #AlphaFold - how cool! See: www.youtube.com/live/HnT1VWz...
- Reposted by Scott SoderlingGoogle’s quantum computer chip called Willow, needed less than five minutes to perform a mathematical calculation that one of the world’s most powerful supercomputers could not complete in 10 septillion years, a length of time exceeding the age of the known universe. www.nytimes.com/2024/12/09/t...
- Amazing AI tool by Rohit Singh's lab at Duke. Shrink or Supersize your protein and retain functions- all based on protein language models.
- Congratulations to @youngsuko9.bsky.social on their top-10 placement in Adaptyv Bio's EGFR-binder competition! It's an elegant pipeline-- using our protein-design method Raygun to expand and modify the template (EGF), then filtering with ProTrek. foundry.adaptyvbio.com/competition 1/
- Reposted by Scott SoderlingWe are hiring a Director for the Carolina Institute for Neurodevelopmental Disorders. This is a highly prestigious position and a great opportunity for a leader! This could be you! unc.peopleadmin.com/postings/286...
- Been talking about exploring active learning for some projects. EVOLVEPro suggests we really should. www.science.org/doi/10.1126/...
- Reposted by Scott SoderlingThe big one is out! So over the moon to see our latest work with Stéphane Vassilopoulos published in Science. Check out how we reveal the unique architecture of clathrin-coated pits and endocytosis at the axon initial segment: www.science.org/doi/10.1126/...
- Reposted by Scott SoderlingThrilled to announce Boltz-1, the first open-source and commercially available model to achieve AlphaFold3-level accuracy on biomolecular structure prediction! An exciting collaboration with Jeremy, Saro, and an amazing team at MIT and Genesis Therapeutics. A thread!
